Will Colin Kaepernick be a running quarterback or a pocket quarterback in 2015? The answer, quarterbacks coach Steve Logan said Thursday, is yes.

Logan , who along with the other 49ers assistants spoke to reporters for the first time this offseason, said he treasures quarterbacks who can beat defenses with their legs and that Kaepernick will not be discouraged from taking off from the line of scrimmage.

The trick is knowing when to spring.

“The operative word is ‘discernment,’” Logan said. “You’ve got a trump card available to you that some quarterbacks don’t. What we need to learn is when to use the trump card and when not to. If we use the trump card too much, you’ll devolve as a pocket passer. If you learn to use it at the appropriate times, you can really blossom as a pocket passer.”

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Logan met 49ers coach Jim Tomsula in 2004 when they were assistants on the Berlin Thunder of NFL Europe. When Tomsula became the head coach of the Rhein Fire two years later, he hired Logan to run his offense, and they have remained friends.

Logan, 62, also spent 14 seasons at East Carolina, first as the school’s running backs coach and then as the head coach for 11 seasons. He mentored two quarterbacks, Jeff Blake and David Garrard, who played in the NFL and who, like Kaepernick, could beat defenses with their arms and feet.

Logan said running quarterbacks give defenses more to worry about. A defensive coordinator must reassess his blitz coverages and figure out who will keep track of the quarterback when playing man-to-man coverage.

“And this is where we’ve seen Colin Kaepernick and Aaron Rodgers and all these mobile quarterbacks who can really do damage to defenses by pulling the football down when everybody’s covered and go get something maybe a Peyton Manning or a more pocket-oriented quarterbacks is not capable of getting,” Logan said. “And that’s not a knock on anybody. It’s just I really prefer to have that bonus attached to the quarterback position.”

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Kaepernick has spent much of the offseason learning how to be a better pocket passer. He has worked on his mechanics but also spent plenty of classroom time with former quarterback Kurt Warner, a noted pocket passer, in an effort to become better at reading defenses and making decisions.

There is no disconnect, Logan said.

The 49ers’ goal this season, he said, is to become a balanced offense, not in the sense of attempting a similar number of passes and runs, but in being able to run the ball when situations call for it and throw when given the opportunity. The same philosophy applies to the quarterback.

One major change: They will attempt more downfield passes.

Over the past four seasons, the 49ers targeted wide receivers deep downfield less than any other team. During the offseason, they added two speedsters at the position, Torrey Smith and Jerome Simpson, plus Reggie Bush, who leads active running backs in career receptions.

“Explosion plays – that’s where you make a living,” Logan said.

Logan said he and offensive coordinator Geep Chryst would trade a high completion percentage during some games this season for big gains passing.

Logan offered a scenario in which Kaepernick completed only 48 percent of his passes but had three “explosion plays” that created 21 points.

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